Riboswitches That Sense Cyclic Di-GMP

Riboswitches are almost always located in the 5' untranslated regions (UTRs) of messenger RNAs, where they typically control either transcription elongation or translation initiation of genes whose protein products synthesize or transport the regulatory ligand. GEMM RNAs were very promising candidate riboswitches because, in part, they contain regions of high sequence conservation interspersed with secondary structure elements supported by covariation. The first technique employed to test the candidate riboswitch was an assay called in-line probing, which can be used to assess structural changes in riboswitches in response to ligand binding. The recognition that GEMM RNAs function as cyclic di-GMP (c-di-GMP) riboswitches facilitates the identification of entire regulons of genes that are likely controlled by changing concentrations of second messenger. Regardless of these complications, the association of genes with sequences that appear homologous to validated c-di-GMP riboswitches may help researchers identify and examine processes that are likely to be regulated by the second messenger. V. cholerae carries two elements that conform to the c-di-GMP riboswitch consensus. The identification of c-di-GMP riboswitches will allow researchers to more easily identify processes that are regulated in response to changing concentrations of the second messenger. Furthermore, some of these riboswitches already have proven to function in new hosts and, therefore, may function as useful biosensors that can report the concentrations of c-di-GMP in cells in different genetic backgrounds or under different environmental conditions. Riboswitches that bind to c-di-GMP have been identified that appear to control a great diversity of genes associated with second messenger signaling.